The Histology and Light Microscopy Core provides technical assistance, training, consultation, and assistance with all aspects of experimental design, sample preparation, image processing, and data analysis. The core is equipped with state-of-the-art technologies and expertise in histology, high-resolution histological imaging, confocal microscopy, light sheet microscopy, spinning disk microscopy, and optical projection tomography.

Our team strives to provide you with the knowledge and equipment you need to perform your experiment successfully.

For optimal results, reach out to our staff in the planning stages of your experiments.

Biology is a beautiful thing, and we want to work with you to make it that way!

Contact

Blaise Ndjamen, PhD
Core Director
Email

 

Services Provided

  • Histology: tissue processing (paraffin and frozen), embedding, sectioning, staining and whole slide scanning.
    Staining: H&E, IHC, ISH, TUNEL, RNAscope, 10x Visium, and special staining.
  • Advanced Microscopy (on live and fixed samples): Confocal, spinning disk, light-sheet, super-resolution, automated whole slide scanning, widefield microscopy, tissue clearing and volumetric imaging.
  • Quantitative Data and Image Analysis: using Imaris, Volocity, ImageJ/FIJI, MatLab, and Python
  • Training, consulting, and collaborations

Core Members

Marcella Foti
Research Technologist II

Rose Guerrero
Research Technologist III

Blaise Ndjamen
Core Director

Fengrong Yan
Senior Research Technologist

Capabilities

 

Histology: Histology can be a complicated and confusing subject. All steps from tissue dissection and fixation through processing, sectioning, and staining are important to get right. When tissue is removed from the body, there is a rapid activation of proteolytic enzymes involved with tissue decomposition. In order to view tissues in a state that is as “life-like” as possible, the tissue must be processed immediately. In most circumstances, this is done through immediate fixation using paraformaldehyde or formalin

Microscopy: The Microscopy team provides training and support services for independent users, as well as more advanced microscopy imaging services, 3D deconvolution and rendering, image analysis, and quantitation. Our staff provides consultation and assistance with all aspects of experimental design, sample preparation, imaging, data processing and analysis.

 
 

Quantitative Data and Image Analysis (using Imaris, Volocity, ImageJ/FIJI, MATLAB)

Training, Consultation & Collaboration

 

Equipment

Learn how our experts can support your research.

Lightsheet/Single Plane Illumination Microscopy

Zeiss Z1 Light Sheet Microscope (Fin Whale)

Zeiss Z1 Light Sheet Microscope

What

  • Light Sheet Fluorescence Microscope
  • For both aqueous and cleared samples
  • Dual cameras for 2-color simultaneous acquisition (405nm, 488nm, 561nm, 640nm lasers)

Why

Sample requirements:

  • Typically embedded in agarose; either aqueous or pre-cleared (Clarity, PACT, etc.)
  • Samples usually fluorescently labeled
  • Sample preparation can require extensive optimization

Suitable applications:

  • High-speed fixed or live-cell imaging (>100fps)
  • Imaging large, thick samples at high resolution with extremely low-bleach, low phototoxicity
  • Long-term live-cell imaging (>6 hours)
  • Isotropic resolution- best possible 3D reconstruction

Not good for:

  • High magnification (max = 40x)
  • Simple experiments- time, labor, and data intensive!

Confocal Microscopy

Leica SP5 inverted confocal microscope (Eagle}
Zeiss Cell Observer Spinning Disk Confocal Microscope (Hare)
Zeiss LSM880 with Airyscan (Tarsier)
Olympus Fluoview FV3000 Confocal Microscope (Snow Leopard)

Leica SP5 Inverted Confocal Microscope

What

  • Point-scanning inverted confocal microscope system
  • Laser (458nm, 488nm, 514nm, 543nm, 633nm) and metal halide illumination
  • Motorized stage and incubation (temperature control only)

Why

Sample types:

  • Chamber slides, 35mm dishes, or optical-quality well plates

Applications:

  • Fixed and live-cell confocal imaging
  • Up to 3 channels simultaneous acquisition
  • AOBS tunable beam-splitter for great flexibility with fluorophore combinations
  • Live-cell dynamics (FRAP, FRET, GCaMP)
  • Multipositional acquisition and tiling multiple images for large sample areas
  • Imaging individual cells at high magnification (63x, 100x)

Not good for:

  • Imaging DAPI or other dyes requiring 405nm excitation
  • Live-cell imaging requiring CO2 control
  • Very thick samples (>100µm)
  • Low-light fluorescence imaging
  • High-speed fluorescence imaging

Zeiss Spinning Disk Confocal Microscope

What

  • Spinning disk confocal and wide-field epifluorescence system for live cell imaging.
  • Laser (405nm, 488nm, 561nm, 640nm), metal halide and LED illumination
  • Definite focus
  • DirectFRAP

Why

Sample types:

  • Chamber slides, 35mm dishes or optical-quality well plates

Applications:

  • High speed, live-cell confocal imaging
  • Live-cell dynamics (FRAP, FRET, GCaMP, FURA), imaging
  • Imaging individual cells at high magnification (63x, 100x)

Not good for:

  • Thick samples (>50um)
  • Low magnification, large field-of-view imaging

Zeiss LSM880 Super-Resolution Confocal Microscope

What

  • Point-scanning confocal microscope
  • Airyscan detector for increased resolution (>120nm lateral), sensitivity
  • Multiple laser lines (405nm, 445nm, 488nm, 514nm, 561nm, 638nm)
  • Definite focus
  • Objective inverter for using dipping lenses

Why

Sample types:

  • Chamber slides, 35mm dishes or optical-quality well plates

Applications:

  • Scanning confocal imaging for mid-speed (13 fps) live-cell imaging
  • Live-cell fluorescent dynamics (i.e. FRAP, FRET, GCaMP)
  • Imaging individual cells at high resolution, any magnification
  • Multipositional acquisition and tiling multiple images for large sample areas

Not good for:

  • Very thick samples (>100µm)
  • Very high-speed imaging (>10fps)

Olympus Fluoview FV3000 Confocal Microscope

What

  • Point-scanning confocal microscope
  • Both Galvo & Resonance scanning for high speed imaging
  • Multiple laser lines (405nm, 445nm, 488nm, 514nm, 594nm, 561nm, 638nm)
  • Definite focus with Z drift correction function
  • Inverted microscope with motorized (x,y,Z) stage
  • >Incubation chamber (CO2, Temperature & Humidity) for both short & long live cell/tissue imaging

Why

Sample types:

  • Chamber slides, 35mm dishes or optical-quality well plates
  • Combo 35mm & Chambered slide holder
  • Both live & fixed tissues/cells

Applications:

  • Scanning confocal imaging for live and fixed -cell, organoid and tissue imaging
  • Live-cell fluorescence dynamics (i.e. FRAP, FRET, GCaMP)
  • Imaging individual cells at high resolution, any magnification
  • Multipositional acquisition and tiling multiple images for large sample areas

Not good for:

  • Very thick samples (>100µm)
  • Very high-speed imaging (>10fps)

Widefield Microscopy

Leica Versa 200 Slide Scanner (Octopus)
Nikon Eclipse E600 Upright Microscope (Chameleon)
Keyence Automated Epifluorescence Microscope (Coyote 1)
Keyence Inverted Epifluorescence Microscope (Coyote 2 and 3)
Zeiss AxioObserver Z1 inverted epifluorescence microscope (Cuttlefish)
Zeiss live cell inverted epifluorescense microscope (Tortoise)

Leica Versa 200 Automated Slide Scanner

What

  • Automated slide scanner with wide-field fluorescence and brightfield imaging
  • Metal halide illumination; filters for DAPI, GFP, RFP, and Cy5
  • High sensitivity RGB and monochrome camera
  • 5x, 10x, 20x, 40x air objectives and 63x oil objective (with auto-oiler)

Why

Sample types:

  • Slides

Applications:

  • Automated whole slide imaging for up to 200 slides per run
  • Multipositional acquisition and tiling for large sample areas

Not good for:

  • Long term live-cell imaging
  • Thick samples (>50um)

Nikon Eclipse E600 Upright Microscope

What

  • Wide-field upright epifluorescence and full-color brightfield imaging system
  • Metal halide illumination; filters for DAPI, FITC, and Texas Red
  • RGB and monochrome Retiga camera with Qcapture acquisition software

Why

Sample types:

  • Slides

Applications:

  • Epifluorescence and brightfield imaging for fixed samples

Not good for:

  • Live-cell imaging
  • Tissue cultures plates and dishes
  • Time-lapse microscopy
  • Low-light fluorescence imaging

Keyence Automated Epifluorescence Microscope

What

  • Automated inverted wide-field epifluorescence and brightfield imaging system
  • Metal halide illumination; filters for DAPI, GFP, RFP, and Cy5
  • High sensitivity RGB and monochrome camera

Why

Sample types:

  • Slides or 35mm dishes
  • Tissue culture plates
  • Petri dishes

Applications:

  • Epifluorescence imaging for fixed and live-cell samples
  • Multipositional acquisition and tiling multiple images for large sample areas
  • Structured illumination for increased resolution (pseudo-confocal)
  • Phase contrast and oblique illumination for high contrast brightfield imaging

Not good for:

  • Long term live-cell imaging
  • Thick samples (>50um)

Keyence Inverted Epifluorescence Microscope

What

  • Automated wide-field epifluorescence system
  • Metal halide illumination; filters for DAPI, GFP, RFP, and Cy5

Why

Sample types:

  • Slides or 35mm dishes

Applications:

  • Epifluorescence imaging for fixed and live-cell samples
  • Tiling multiple images for large sample areas

Not good for:

  • Long term live-cell imaging
  • Thick samples (>50um)
  • Plastic tissue culture plates

Zeiss AxioObserver Z1 Inverted Microscope

What

  • Wide-field epifluorescence system for fixed and live-cell imaging
  • Metal halide illumination; filters for DAPI, GFP, RFP, and Cy5
  • Definite focus, motorized stage, and stable incubation (temperature and CO2 control)
  • Polarizing filter for imaging birefringence

Why

Sample types:

  • Slides, 35mm dishes, or tissue culture well plates

Applications:

  • Long-term live-cell imaging experiments
  • Multipositional acquisition and tiling multiple images for large sample areas

Not good for:

  • High-speed live-cell imaging
  • Thick samples (>50um)

Zeiss AxioObserver Z1 Inverted Microscope

What

  • Wide-field inverted epifluorescence system for fixed and live cell imaging
  • Metal halide illumination; filters for DAPI, GFP, RFP, and Cy5
  • Motorized stage and full incubation (temperature and CO2 control)
  • Flash4.0 sCMOS camera for low-light and high-speed imaging

Why

Sample types:

  • Slides, 35mm dishes, or tissue culture well plates

Applications:

  • Epifluorescence imaging for fixed and live-cell samples
  • Short term time-lapse imaging
  • Multipositional acquisition and tiling multiple images for large sample areas

Not good for:

  • Long term live-cell imaging
  • Thick samples (>50um)

Tissue Clearing

LifeCanvas Active Tissue Clearing System (Jellyfish)

LifeCanvas Active Tissue Clearing System

What

  • EasyGel - Tissue Gel Hybridization System
  • Integrated temperature control and vacuum
  • 8 samples at once
  • SmartClear II - Active Clearing System
  • Maximum preservation of fluorescent protein (FP) signals
  • Based on stochastic electrotransport technology developed at MIT (Kim et al., PNAS, 2015)

Why

Sample types:

  • Fixed tissues > 500um
 

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FAQs

How Can I Get a Quote for My Project?

  1. Login into your iLab account
  2. Initiate a service request
  3. Use the temporary PO number 11111 to finalize and submit your service request
  4. Email the core after your service request is submitted with the temporary PO to receive a formal quote
  5. Use the quote to generate a formal PO by your lab or organization’s financial department
  6. Use the valid PO to update your iLab account profile and billing or financial information
  7. Email the core a PDF copy of your formal PO

What Type of Tissue Can Be Submitted to the Core Lab for Processing?

We accept a large variety of tissue types including regular soft tissues as well as bones, cells, and organoids pre-embedded in histogel or in suspension. All tissues must be fixed prior to submission.

Should I Fix My Samples Prior to Submitting Them to the Core, and What Is the Best Way to Fix Them?

Yes, all tissue should be fixed prior to submission. Most tissues do well with fresh perfusion followed by 4% PFA fixation overnight in the fridge. Common exceptions are brain and bone samples, which require extended fixation. Email us for more information.

How Do I Submit My Samples?

Formalin-fixed samples must be fixed for paraffin embedding (FFPE), and samples should be fixed and stored in 70% ethanol. To prepare cryo-samples, fixed tissues are submitted in 30% sucrose. The sample container must be leak-proof, and labeled with the iLab request track numbers.

Cassettes should be hand labeled with #2 pencil or solvent-resistant markers (we use the KP Marker Plus, from Scutek laboratories).

Let us know if you want your container returned, otherwise it will be recycled. You can provide your own slide boxes or purchase them from the core.

Any antibodies you provide must also be labeled.

Contact the core for the 10x Genomics Visium sample preparation

Can Samples Be Sent by Mail?

All samples must be dropped off in person.

When Will My Project Be Done?

Standard turn-around time is typically 10–20 working days from the date the samples are dropped off and received by the core (not the project submission date via iLab), depending on the size of the order and how many requests we have in our queue.

Rush orders turn-around is 5–10 days

Note that these are estimates and turn-around times can be longer due to the complexity and size of the project and our current workload, in addition to delays due to the COVID-19 pandemic. 

How Do I Know When My Samples Are Ready?

You will be noticed by iLab mail. Pick up by the drop-off area, in room 367 at Upward Research Labs. Remember to pick up your antibodies as well!

Does the Core Provide Pathology Assessment?

Our core does not provide pathology assessment.

How Do I Pay for Services?

When you create an iLab account, you will provide a valid PO. We do not accept credit cards or cash.

Can I Use the Core Equipment (Scopes, Cryostat, Microtome) Independently?

All users must be trained by staff prior to accessing and using any equipment in the core.

How Do I Request Training?

First, set up an iLab account. Once you’ve created your account, fill out the instrument training request.

Once you send the request, it typically takes 1-2 weeks to schedule a training session.

Our training protocol is a 2-step process: the 1st session is more general and covers care and handling of the microscope. The 2nd session is more project-specific. At the end of these two training sessions, we then evaluate the comfort level of the trainee with the microscope before granting them the "assisted/dependent” (conditional access) or unassisted/independent user status with full access to the calendar.

How Do I Access the Core?

The core is located in room 367 at Upward Research Labs. Our hours are Monday—Friday, 8:30am—5:00pm,

Instructions

Before entering the building, you must read Upward Research Labs' COVID-19 safety protocol and attest that you have no symptoms and will adhere to Upward Research Labs' COVID-19 protocols. 

Sign into reception in the lobby and the receptionist will call the core. For speedier entry to the building, email the core prior to your arrival and we will plan to meet you in the lobby to escort you.

When Should I Cite a Core Facility in a Publication, Presentation, or Poster?

We ask that you be generous with your citations. If you have any questions, reach out to one of the core managers.

Examples of when you should cite a core could include acknowledgement of:

  • Space
  • Equipment
  • Purchased core reagents/media
  • Services
  • If a core staff member assists you in the design or execution of your experiments

How Do I Access the Core's iLab and Request a Service as a UC San Francisco User?

  1. Login to iLab using your UC San Francisco credentials
  2. Click on the menu on the top left of the page
  3. Click core facilities
  4. Change view to "Cores at Other Institutions"
  5. Enter "Upward Research Labs" in the search box
  6. Find the link for the Histology and Light Microscopy Core and select

To Request a Service

  1. Visit the core's iLab page 
  2. Once logged in, select "request service"
  3. Include your lab's or PI's purchase order number in your request

When Can I Drop-Off or Pick-Up My Samples and Data?

Samples can be submitted Monday through Thursday from 10am–3pm or on Fridays by appointment.

You should contact the core before you drop off your samples. Email us at histology@upwardresearchlabs.com or call 415.734.2012.